EP1700114A2 - Procede d'enrichissement/de separation de proteine ou de peptide - Google Patents

Procede d'enrichissement/de separation de proteine ou de peptide

Info

Publication number
EP1700114A2
EP1700114A2 EP04808028A EP04808028A EP1700114A2 EP 1700114 A2 EP1700114 A2 EP 1700114A2 EP 04808028 A EP04808028 A EP 04808028A EP 04808028 A EP04808028 A EP 04808028A EP 1700114 A2 EP1700114 A2 EP 1700114A2
Authority
EP
European Patent Office
Prior art keywords
electron
peptide
amino acid
protein
group
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP04808028A
Other languages
German (de)
English (en)
Other versions
EP1700114A4 (fr
Inventor
Makoto Watanabe
Eiichi Matsuo
Chikako Toda
Osama Nishimura
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Shimadzu Corp
Original Assignee
Shimadzu Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Shimadzu Corp filed Critical Shimadzu Corp
Publication of EP1700114A2 publication Critical patent/EP1700114A2/fr
Publication of EP1700114A4 publication Critical patent/EP1700114A4/fr
Withdrawn legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K1/00General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/14Extraction; Separation; Purification
    • C07K1/24Extraction; Separation; Purification by electrochemical means

Definitions

  • the present invention relates to the field in proteomics or exhaustive analysis for protein.
  • BACKGROUND ART Peptide mass fingerprinting (PMF)
  • PMF BACKGROUND ART Peptide mass fingerprinting
  • a technique that combines 2D-PAGE with the benefit of mass spectrometer has thus far been a main analytical technique used in the field of proteomics and exhaustive analysis of protein.
  • the differential display analysis using 2D-PAGE has been used as a tool for determining relative quantification of proteins.
  • These techniques have defects, however, in terms of the reproducibility of protein separation and gel staining, and the solubility of proteins.
  • exhaustive analysis of protein that employs stable isotopes has been developed as an approach to next-generation protein analysis .
  • sulfenyl compounds are known as selective labeling reagents for tryptophan residues.
  • NBSCl 2-nitrobenzene sulfenyl chloride
  • Proteins in one sample are then labeled with a non-labeled NBSCl reagent at the tryptophan residues and proteins in the other sample are labeled with a R elabeled NBSCl reagent at the tryptophan residues.
  • the two labeled samples are mixed and the mixture is subjected to- enzymatic digestion by trypsin.
  • the peptides containing tryptophan residues are separated and are subjected to mass spectrometry.
  • the peptides detected as paired peaks that have 6 daltons mass difference are then subjected to sequence analysis and the relative quantification of the peptides (Hiroki
  • the invention thus is based on a principle that proteins or peptides contaning ⁇ electron group-containing amino acid residues can be selectively separated by taking advantage of the ⁇ - ⁇ electron interactions between the ⁇ electron- containing media and the proteins or the peptides containing an amino acid residue with a ⁇ electron group.
  • the present invention thus comprises the following aspects: (1) A method for enrichment/separation of a protein or a peptide, comprising separating a protein or a peptide containing an amino acid residue with a ⁇ electron-containing group by using a media with a ⁇ electron-containing group. (2) The method according to (1), wherein the amino acid residue with a ⁇ electron-containing group is tryptophan residue. (3) The method according to (1) or (2), wherein the ⁇ electron-containing group of the media is phenyl group.
  • a method for enrichment/separation of a protein or a peptide comprising separating a protein or a peptide containing an amino acid residue with a ⁇ electron-containing modifying group, which is modified with a ⁇ electron-containing compound, by using a media with a ⁇ electron-containing group.
  • the ⁇ electron-containing compound is a sulfenyl compound having ⁇ electrons.
  • the sulfenyl compound is 2-nitrobenzene sulfenyl chloride.
  • a method for enrichment/separation of a peptide comprising the steps of: fragmenting a protein or a peptide containing an amino acid residue with a ⁇ electron-containing group, to obtain a fragmented sample solution which contains a peptide fragment containing the amino acid residue with the ⁇ electron-containing group and a peptide fragment with no ⁇ electron-containing group; and exposing the fragmented sample solution to a media with a ⁇ electron-containing group, to separate the peptide fragment containing the amino acid residue with the ⁇ electron-containing group from the peptide fragment with no ⁇ electron-containing group.
  • a method for enrichment/separation of a peptide comprising the steps of: modifying a protein or a peptide with a ⁇ electron- containing compound to obtain a sample solution which contains a protein or a peptide containing an amino acid residue with a ⁇ electron-containing modifying group; fragmenting the protein or the peptide containing the amino acid residue with the ⁇ electron-containing modifying group, to obtain a fragmented sample solution which contains a peptide fragment containing the amino acid residue with the ⁇ electron-containing group and a peptide fragment with no ⁇ electron groups; and exposing the fragmented sample solution to a media with a ⁇ electron-containing group, to separate the peptide fragment containing the amino acid residue with the ⁇ electron-containing group from the peptide fragment with no ⁇ electron-containing group.
  • the present invention makes it possible to enrich/separate such proteins or peptides in a highly selective manner.
  • the method of the present invention enables more effective and accurate proteome analysis of various biological samples, including determination of relative quantification and sequence analysis of peptides or proteins in biological samples using a mass spectrometer.
  • Fig. 1 shows a MALDI-TOF MS spectrum of Example prior to enrichment of peptide fragments containing labeled tryptophan residues.
  • Fig. 2 shows MALDI-TOF MS spectra for the first fraction to the sixth fraction of twelve wash fractions collected in Example during washing with a wash buffer.
  • Fig. 3 shows MALDI-TOF MS spectra for the seventh fraction to the twelfth fraction of twelve wash fractions collected in Example during washing with the wash buffer.
  • Fig. 4 shows (a) MALDI-TOF spectra for the first fraction to the fifth fraction eluted in Example with an elute buffer, and (b) an enlarged view of one of the paired peaks indicated by arrows in (a) .
  • the present invention concerns a enrichment/separation technique for use in chromatography of proteins or peptides that takes advantage of the ⁇ - ⁇ electron interactions between ⁇ electron groups of amino acid residues in proteins or peptides to be enriched/separated and ⁇ electron groups of a media to serve as the stationary phase of the chromatography.
  • proteins or peptides containing amino acid residues with ⁇ electron- containing groups can be enriched/separated in a selective manner.
  • the ⁇ electron-containing groups are not limited, aromatic hydrocarbon groups are preferred.
  • the amino acid residue with ⁇ electron-containing group is especially preferably tryptophan residue.
  • the amino acid residue with the ⁇ electron-containing group may be an amino acid residue of a protein or a peptide which is previously modified with a ⁇ electron compound.
  • the ⁇ electron compound for modifying amino acid residues is preferably a sulfenyl compound.
  • a sulfenyl compound can selectively modify tryptophan residues, preferred amino acid residues of the present invention.
  • the sulfenyl compound may be any sulfenyl compound that is represented by the general formula R-S-X (where R represents an organic group, and X represents a leaving group) , it is preferred that the organic group R be an aromatic hydrocarbon group.
  • the sulfenyl compound include 2-nitrobenzene sulfenyl chloride, 4-nitrobenzene sulfenyl chloride, 2,4- benzene sulfenyl chloride, and 2-nitro-4-carboxybenzene sulfenyl chloride. Of these, 2-nitrobenzene sulfenyl chloride shown by the following structural formula (I) is particularly preferred:
  • the media for separating the above-described protein or peptide containing the amino acid residues with ⁇ electron groups has a ⁇ electron- containing group.
  • the ⁇ electron-containing group of the media is not limited, aromatic hydrocarbon groups, such as phenyl group, are preferred.
  • aromatic hydrocarbon groups such as phenyl group
  • the media is exposed to the above- described protein or peptide with ⁇ -electron groups .
  • a YMC-PackPh column (YMC Corp.) packed with the media with phenyl groups to serve as the solid phase may be used.
  • the present invention can be used in the exhaustive analysis of protein for various biological samples, including determination of relative quantification and sequence analysis of peptides or proteins using a mass spectrometer.
  • two labeling reagents a stable isotope-labeled form and an non-labeled form of the above-described sulfenyl compound
  • Two series of biological samples e.g., normal cells and cancer cells
  • One of the samples is then performed tryptophan-labeling treatment with the stable isotope-labeled form of the above sulfenyl compound, and the other is performed tryptophan- labeling treatment with the non-labeled form of the same compound.
  • the labeled samples are mixed with each other and the mixture is subjected to fragmentation. This results in a mixture containing labeled peptide fragments along with non-labeled peptide fragments. Subsequently, the labeled peptide fragments are separated from the peptide fragment mixture, and this is where the present invention is preferably applied. Specifically, Using a media with for example phenyl groups, the labeled peptide fragments in the peptide fragment mixture are allowed to selectively adsorb onto the media, the other non-labeled peptide fragments are washed off, and the adsorbed labeled peptide fragments are subsequently eluted. In this manner, the labeled peptide fragments can selectively be separated.
  • the separated labeled peptide contains two types of labeled peptides: one labeled with the stable isotope-labeled compound and the other labeled with the non-labeled compound.
  • the two peptides are detected in mass spectrometry as paired peaks that have 6 daltons mass difference which corresponds to the mass difference between the two labeling reagents.
  • the paired peaks also have an area ratio corresponding to the relative quantification of the two labeled peptides.
  • the detected paired peak allows determination of the relative quantification of the peptides and sequence analysis.
  • conventional Sephadex-based reversed-phase chromatography techniques often result in a deviation in the resolution and the reproducibility of the results. This drawback can be eliminated by the use of the method of the present invention.
  • the method of the present invention therefore, is more practical than conventional techniques and enables more effective and accurate protein analysis.
  • Fig 1 entitled "Before the enrichment of peptide fragments containing labeled tryptophan residues".
  • horizontal axis represents the mass/charge ratio and vertical axis represents the intensity of the fragment ions.
  • YMC-Pack Ph packing material YMC Corp.
  • the paired peaks also have an area ratio of 1:2, which corresponds to the mixed ratio of the labeled and non- labeled peptides. These paired peaks are detected only in Elute fractions (1) through (5) . These figures indicate that the desired peptide fragments containing labeled tryptophan residues can be eluted to the Elute fraction in a selective manner by using the method of the present invention.
  • the peptide containing labeled tryptophan is prepared as the protein or peptide containing amino acid residue with ⁇ electron- containing modifying group, by modifying rat serum with nitrobenzenesulfenyl chloride; separated by using the media with phenyl group as the ⁇ electron-containing group; and used for mass spectrometry analysis.
  • the present invention is not limited to the above- described peptide, but may be applied to any protein and peptide containing ⁇ electron-containing group or ⁇ electron-containing modifying group. Also, the present invention is not limited to the above-described media, but may be used any media with ⁇ electron-containing group.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biochemistry (AREA)
  • Electrochemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Peptides Or Proteins (AREA)

Abstract

La présente invention concerne une substance permettant de retenir de manière hautement sélective des protéines ou peptides à enrichir/séparer, ainsi qu'un procédé d'enrichissement/de séparation sélectifs de protéines ou de peptides à l'aide d'une telle substance. Un procédé d'enrichissement/de séparation d'une protéine ou d'un peptide, comportant la séparation d'une protéine ou d'un peptide contenant un résidu d'acide aminé ayant un groupe contenant un électron par l'utilisation d'une substance ayant un groupe contenant un électron . De préférence, le résidu d'acide aminé est un résidu de tryptophan ou un résidu de tryptophan modifié par un composé sulfényle, et la substance est un substance ayant un groupe phényle.
EP04808028A 2003-12-25 2004-12-21 Procede d'enrichissement/de separation de proteine ou de peptide Withdrawn EP1700114A4 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
JP2003430898A JP2005189104A (ja) 2003-12-25 2003-12-25 タンパク質又はペプチドの濃縮分離法
PCT/JP2004/019677 WO2005062725A2 (fr) 2003-12-25 2004-12-21 Procede d'enrichissement/de separation de proteine ou de peptide

Publications (2)

Publication Number Publication Date
EP1700114A2 true EP1700114A2 (fr) 2006-09-13
EP1700114A4 EP1700114A4 (fr) 2007-07-11

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Family Applications (1)

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EP04808028A Withdrawn EP1700114A4 (fr) 2003-12-25 2004-12-21 Procede d'enrichissement/de separation de proteine ou de peptide

Country Status (4)

Country Link
US (1) US20070112181A1 (fr)
EP (1) EP1700114A4 (fr)
JP (1) JP2005189104A (fr)
WO (1) WO2005062725A2 (fr)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN100374857C (zh) * 2006-01-26 2008-03-12 复旦大学 快速富集痕量多肽或蛋白质并实现鉴定的方法
WO2007108140A1 (fr) * 2006-03-22 2007-09-27 Shimadzu Corporation Procede d'identification et de quantification pour un echantillon de proteine a l'aide d'une electrophorese et d'une spectrometrie de masse
WO2008015768A1 (fr) * 2006-08-02 2008-02-07 Shimadzu Corporation Procédés permettant de quantifier les résidus tryptophane oxydés dans un échantillon et de déterminer leur position
US20090288015A1 (en) * 2008-03-13 2009-11-19 Robb Fujioka Widgetized avatar and a method and system of creating and using same
CN105890964B (zh) * 2015-01-26 2018-08-21 中国科学院大连化学物理研究所 一种高选择、高灵敏富集衍生的化学选择纳米探针及其制备方法和应用

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000068395A2 (fr) * 1999-05-10 2000-11-16 Cp Kelco Aps Sulfohydrolases, sequences correspondantes d'acides amines et de nucleotides, preparations de sulfohydrolases, procedes, et leurs produits
WO2001086306A2 (fr) * 2000-05-05 2001-11-15 Purdue Research Foundation Peptides a signature a affinite selective permettant l'identification et la quantification de proteines

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP3494763B2 (ja) * 1995-07-26 2004-02-09 ナカライテスク株式会社 液体クロマトグラフィー用充填剤及びそれを用いた分離方法
SE0104353D0 (sv) * 2001-12-19 2001-12-19 Amersham Biosciences Ab Separation method

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000068395A2 (fr) * 1999-05-10 2000-11-16 Cp Kelco Aps Sulfohydrolases, sequences correspondantes d'acides amines et de nucleotides, preparations de sulfohydrolases, procedes, et leurs produits
WO2001086306A2 (fr) * 2000-05-05 2001-11-15 Purdue Research Foundation Peptides a signature a affinite selective permettant l'identification et la quantification de proteines

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
See also references of WO2005062725A2 *
VERONESE F M ET AL: "SELECTIVE SEPARATION OF TRYPTOPHAN DERIVATIVES USING SULFENYL HALIDES" ACTA VITAMINOLOGICA ET ENZYMOLOGICA, MILAN, IT, vol. 29, no. 1-6, 1975, pages 243-247, XP008062973 ISSN: 0300-8924 *

Also Published As

Publication number Publication date
WO2005062725A3 (fr) 2005-11-17
WO2005062725A2 (fr) 2005-07-14
JP2005189104A (ja) 2005-07-14
EP1700114A4 (fr) 2007-07-11
US20070112181A1 (en) 2007-05-17

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